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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__databases_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/objutils/blast_databases.cpp Source File

vector<string>

;

(!istr.eof()) {

(str_line.empty())

db_name, db_string;

(db_string.size() > 1 && db_string[0] ==

&& (db_string[1] ==

|| db_string[1] ==

)) {

mru_dbs.push_back(db_name);

(notn->

() != m_JobId)

;

CNetBlastLoadDBListJob(

& dir,

& dbtree);

~CNetBlastLoadDBListJob() {}

unordered_map<string, string> TDbMap;

EJobState

();

x_SaveBlastDataBases(

&

);

(

);

CNetBlastLoadDBListJob::CNetBlastLoadDBListJob(

& dir,

& dbtree)

: m_Dir(dir), m_DBTreePath(dbtree)

CNetBlastLoadDBListJob::GetDescr()

;

ex_md5_req->Add(

(

),

(

) );

protocol_info_reply =

.AskGet_protocol_info( *ex_md5_req );

(!md5_param.

() && md5_param->GetValue().IsString())

= md5_param->GetValue().GetString();

err_msg, logMsg =

;

md5file(md5path);

(md5file.Exists()) {

(

<<

<< e.

());

(!cached_md5.empty() && cached_md5 ==

) {

(nuclFile.Exists() && protFile.Exists())

x_CategorizeDBs(dbs);

x_SaveBlastDataBases(

);

err_msg = logMsg + e.

();

}

(

std::exception& e) {

err_msg = logMsg + e.what();

(!err_msg.empty()) {

(

& path,

CNetBlastLoadDBListJob::TDbMap& dbmap)

(CNetBlastLoadDBListJob::TDbMap, it, dbmap) {

= it->first, second = it->second;

CNetBlastLoadDBListJob::x_SaveBlastDataBases(

&

)

(

.empty() || m_NucDbMap.empty())

(

<<

);

(

<<

);

(

<<

<< e.

());

fields.push_back(*it);

(

<<

<<

<<

.

() <<

);

list<CConstRef<CUser_field> > fields;

unordered_map<string, pair<bool, string> > TValidDbNames;

TValidDbNames valid_db_names(db_data.size());

& db_name =

.GetDatabase().GetName();

, db_name, desc;

=

.GetLabel().GetStr();

db_name =

.GetField(

).GetData().GetStr();

desc.append(

.GetField(

).GetData().GetStr());

TValidDbNames::const_iterator dbname_iter = valid_db_names.find(db_name);

(dbname_iter == valid_db_names.end()) {

categorized_dbs.

(db_name);

TDbMap& db = dbname_iter->second.first ? m_ProtDbMap : m_NucDbMap;

string::size_type pos = db_desc.find_first_not_of(

);

(pos != string::npos) {

db_desc.erase(0, pos);

pos = db_desc.find_last_not_of(

);

(pos != string::npos) {

(pos < db_desc.size()) {

name, visible_name;

db_desc, tax_label;

org_name_label =

;

visual_priority_label =

;

m_NucDbMap.reserve(db_data.size());

& db_name =

.GetDatabase().GetName();

(!(db_name ==

|| db_name ==

))

db_desc =

.GetDescription();

visible_name = db_name;

( ! db_desc.empty() && db_name.find(db_desc) == string::npos) {

name +=

+ db_desc +

;

db_desc_trimmed(db_desc);

visible_name +=

+ db_desc_trimmed +

;

visible_name =

(

) + visible_name;

(db_name ==

) {

TDbMap& db =

? m_ProtDbMap : m_NucDbMap;

x_AddCategorizedDBs(dbs, categorized_dbs);

db_desc_trimmed;

& db_name =

->GetDatabase().GetName();

(db_name ==

|| db_name ==

)

(categorized_dbs.

(db_name) != categorized_dbs.

())

db_desc =

->GetDescription();

visible_name = db_name;

( ! db_desc.empty() && db_name.find(db_desc) == string::npos) {

name.append(db_desc);

db_desc_trimmed = db_desc;

visible_name.append(

);

visible_name.append(db_desc_trimmed);

visible_name.append(

);

TDbMap& db = m_NucDbMap;

(tax_id == 9606 || tax_id == 10090) {

vector<string> word_split_vec;

( (*it)->CanGetExtended() ) {

list< CRef< CBlast4_parameter > >::const_iterator pit = ext.

().begin();

(; pit != ext.

().end(); pit++) {

prop_name = (*pit)->GetName();

(prop_name == org_name_label) {

( (*pit)->CanGetValue() ){

(prop_name == visual_priority_label) {

( (*pit)->CanGetValue() ){

(vp > 0 && s.empty()) {

( tax_label.empty() ){

(

<<

<< visible_name);

tax_label = tax_cache.

(tax_id);

(tax_label.empty()) {

(word_split_vec.size() > 2) {

s.append(word_split_vec[0]);

s.append(word_split_vec[1]);

s.append(

);

s.append(visible_name);

(

<<

<< watch.AsSmartString() );

DEFINE_STATIC_MUTEX(s_Mutex)

void s_GetDBTree(const string &file, list< CConstRef< CUser_field > > &fields)

static const char * kBlastDbDataProt

static void s_SaveDbMap(const string &path, const CNetBlastLoadDBListJob::TDbMap &dbmap)

static void s_GetBlastDbMd5(CBlast4Client &client, string &md5)

static const CCompressStream::EMethod kDbDataCompressMethod

static const char * kBlastDbDataNucl

static const char * kBlastDbDataMD5

static void sPrepareDBDescr(string &db_desc)

User-defined methods of the data storage class.

CAppJobError Default implementation for IAppJobError - encapsulates a text error message.

CAppJobNotification Notification send by CAppJobEventTranslator.

void x_UpdateDbMap(bool nuc)

void x_OnJobNotification(CEvent *evt)

static CBLASTDatabases & GetInstance()

vector< string > m_Prot_DefMRU_DBs

const TDbMap & GetDbMap(bool nuc)

void Load(const char *path, const char *dbtree)

vector< string > m_Nuc_DefMRU_DBs

const vector< string > & GetDefaultMRU_DBs(bool nuc_db)

std::unordered_map< string, string > TDbMap

CBlast4_database_info –.

CBlast4_get_databases_ex_request –.

CBlast4_get_protocol_info_request –.

CEvent - generic event implementation TODO TODO - Attachments.

Base class to build jobs with cancel functionality.

static CTaxonCache & GetInstance()

string GetLabel(int tax_id)

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

std::ofstream out("events_result.xml")

main entry point for tests

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static void md5(const char *src, const char *out)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

EMethod

Compression/decompression methods.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

void Info(CExceptionArgs_Base &args)

static string ConcatPath(const string &first, const string &second)

Concatenate two parts of the path for the current OS.

virtual CConstIRef< IAppJobProgress > GetProgress()=0

return progress object, the function shall be synchronized internally.

static CAppJobDispatcher & GetInstance()

virtual CConstIRef< IAppJobError > GetError()=0

Returns IAppJobError object describing internal error that caused the Job to fail.

virtual CRef< CObject > GetResult()=0

Returns the Job Result.

EJobState

Job states (describe FSM)

TJobID StartJob(IAppJob &job, const string &engine_name, IEngineParams *params=NULL)

Starts a Job on the specified engine in "passive mode" - no notifications or progress reports will be...

virtual string GetDescr() const =0

Returns a human readable description of the Job (optional)

#define ON_EVENT(type, id, handler)

virtual EJobState Run()=0

Function that does all the useful work, called by the Engine.

#define END_EVENT_MAP()

Ends definition of Command Map.

#define BEGIN_EVENT_MAP(thisClass, baseClass)

Begins definition of Command Map for CEventHandler-derived class.

TJobState GetState() const

#define MSerial_AsnText

I/O stream manipulators –.

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ eTrunc_End

Truncate trailing whitespace only.

void Run(void)

Enter the main loop.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

@ eStart

Start timer immediately after creating.

static const char label[]

bool IsInteger(void) const

Check if variant Integer is selected.

TInteger GetInteger(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TString & GetString(void) const

Get the variant data.

list< CRef< CBlast4_database_info > > Tdata

bool IsString(void) const

Check if variant String is selected.

@ eBlast4_residue_type_protein

const TData & GetData(void) const

Get the Data member data.

const TFields & GetFields(void) const

Get the variant data.

vector< CRef< CUser_field > > TFields

double value_type

The numeric datatype used by the parser.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

std::istream & in(std::istream &in_, double &x_)

@ eCanceled

Request canceled.

Declares the CRemoteBlast class.

static CNamedPipeClient * client

C++ I/O stream wrappers to compress/decompress data on-the-fly.

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